Lab Meeting (12-01-2017)

Ming Chen

12/01/2017

Overview

Singularity Container

What can container technologies do for you?

Singularity Container

Building containers

Singularity Container

What is cool about Singularity container?

Singularity Container

Demo

Pull a container with R installed on my local computer.

singularity build --writable r.img docker://r-base

Install a testing package as root user.

# run container interactively
singularity shell --writable r.img

# open R and install a testing package
R
install.package('plyr')

Transfer the container to a HPC cluster

scp r.img  mchen33@149.165.156.175:/home/mchen33/r.img

Run the container on the HPC cluster as non-root user.

singularity shell r.img

# check the testing package
R
require('plyr')

Tripal Galaxy and Galaxy workflows

How biologists (assuming none or limited programming experience) can use Galaxy to perform bioinformatics analysis (Demo)

Tripal Galaxy and Galaxy workflows

Launch a Galaxy instance

We are going to use the Docker container created by Björn Grüning.

Launch a docker container which has galaxy installed

docker run -it --rm --name=galaxy_instance \
        -p 80:80 -p 8021:21 -p 8022:22 \
        -e "ENABLE_TTS_INSTALL=True" \
        -e "GALAXY_CONFIG_ADMIN_USERS=example@gmail.com" \
        bgruening/galaxy-stable:17.01 /bin/bash

Start Galaxy

startup

Tripal Galaxy and Galaxy workflows

Tripal Galaxy and Galaxy workflows

Run Galaxy workflows from a Tripal site with Tripal Galaxy module

Updates on R Markdown Galaxy tools

What is a Galaxy tool?

Updates on R Markdown Galaxy tools

What is an R Markdown Galaxy tool?

Updates on R Markdown Galaxy tools

How R Markdown benefits the development of Galaxy tools?

Updates on R Markdown Galaxy tools

Templates available for developing R Markdown Galaxy tools

Updates on R Markdown Galaxy tools

R Markdown Galaxy tools on Tool Shed

Galaxy Tool Generator platform

Galaxy Tool Generator (GTG) is a web-based platform for asisting Galaxy tool development. The components of the GTG platform includes:

Galaxy Tool Generator platform

What GTG platform can do?

Galaxy Tool Generator platform

Start GTG platform

The module is still under development. The code below will eventually replaced by a one line command.

mkdir -p ~/Desktop/galaxy-tool-generator-dev && cd ~/Desktop/galaxy-tool-generator-dev
git clone https://github.com/MingChen0919/galaxy_tool_generator.git
git clone https://github.com/MingChen0919/galaxy_tool_generator_ui.git
git clone https://github.com/galaxyproject/blend4php.git

docker run -it -p 8090:80 --rm --network=galaxy_tool_generator_nw \
            -v $(pwd)/galaxy_tools:/var/www/html/sites/default/files/galaxy_tools \
            -v $(pwd)/galaxy_tool_generator:/var/www/html/sites/all/modules/galaxy_tool_generator \
            -v $(pwd)/galaxy_tool_generator_ui:/var/www/html/sites/all/modules/galaxy_tool_generator_ui \
            -v $(pwd)/blend4php:/var/www/html/sites/all/libraries/blend4php \
            mingchen0919/docker-galaxy-tool-generator '/bin/bash'
   
drush en -y galaxy_tool_generator galaxy_tool_generator_ui

Go to http://127.0.0.1:8090/

Galaxy Tool Generator platform

Create Galaxy tools (demo)

Galaxy Tool Generator platform

Publish to Tool Shed/Test Tool Shed

See https://testtoolshed.g2.bx.psu.edu/ and search for test_galaxy_tool_generator.

Galaxy Tool Generator platform

Install and test tool on a Galaxy instance

cd ~/Desktop/galaxy-tool-generator-dev && mkdir shed_tools
 
docker run -it --rm --network=galaxy_tool_generator_nw --name=galaxy_instance \
        -p 8080:80 -p 8021:21 -p 8022:22 \
        -v $(pwd)/shed_tools:/export/shed_tools \
        -e "ENABLE_TTS_INSTALL=True" \
        -e "GALAXY_CONFIG_ADMIN_USERS=example@gmail.com" \
        bgruening/galaxy-stable:17.01 /bin/bash
startup